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nextflow

by peterk87 ST3

Nextflow workflow syntax highlighting and snippets for Sublime Text 3

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raw.​githubusercontent.​com

sublime-nextflow: Nextflow workflow syntax highlighting and snippets for Sublime Text 3

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Nextflow Syntax Highlighting

Nextflow syntax highlighting extends Sublime Text 3's Groovy syntax with highlighting of:

  • processes
    • input/output/script tags
  • channel highlighting based on matching ch_*
  • some invalid syntax checks (into channel in input tag and from channel in output tag)
  • highlighting special Nextflow functions and variables (workflow, params, task, etc)

Nextflow Snippets

  • proc: process snippet
  • tag: tag directive snippet
  • pub: publishDir directive snippet
  • init: initialize a Nextflow workflow (shebang, some initial params and a help message)
  • illumina: Illumina paired-end reads file pairs channel
  • par: Create a new params parameter (params.<param_name> = <default>)
  • cpus: insert “${task.cpus}” into a script
  • script_path: specify user script (e.g. Python script) to use from scripts/ directory in workflow base directory
  • info: log.info snippet
  • done: on workflow complete or error message